It's important to realize that the menu item Effect > Pathfinder is not the same as using the Pathfinder Panel (Window > Pathfinder).
The menu item strives to keep all artwork "live" and editable. So, while operations are completed, not all operations will result in a change to the actual artwork. The menu applies an Effect to the existing artwork. it does not change the artwork though. If you are seeking to actually alter the artwork, you should choose to use the buttons on the Pathfinder Panel, rather than the menu items. (Note; you could also use the menu item but then you need to be certain to choose Object > Expand to "bake in" the pathfinder effect if needed).
Random extra: Holding down the Option/Alt key while clicking a button on the Pathfinder Panel will make the buttons work the same way the Pathfinder Menu items work.